| Alignments |
Static utility to easily run alignment routines.
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| FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound> |
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile. |
| FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> |
Implements an algorithm which computes a score for a sequence alignment pair.
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| FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound> |
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile. |
| FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound> |
Implements an algorithm which computes a score for a sequence alignment pair.
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| GuideTree<S extends Sequence<C>,C extends Compound> |
Implements a data structure for a guide tree used during progressive multiple sequence alignment.
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| NeedlemanWunsch<S extends Sequence<C>,C extends Compound> |
Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last
Compound of each Sequence). |
| SimpleGapPenalty |
Implements a data structure for the gap penalties used during a sequence alignment routine.
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| SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> |
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| SmithWaterman<S extends Sequence<C>,C extends Compound> |
Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each
Sequence). |
| StandardRescoreRefiner<S extends Sequence<C>,C extends Compound> |
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| SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound> |
Scores using a substitution matrix.
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